Summary of ProcessDB features and philosophy

Summary of ProcessDB features and philosophy

ProcessDB modeling always starts with a diagram. This was a conscious choice based on decades of experience in modeling and experimental biology. Again and again we have found that a mechanistic diagram is the common ground between modeling teams and an experimental teams. ProcessDB diagrams are beautiful because we used state-of-the-art diagram layout tools that are simple to use. ProcessDB diagrams are active, not passive.

The "DB" in ProcessDB stands for "database." But the ProcessDB database is no mere repository of experimental data. Instead, it brings the awesome power of a relational database to the every aspect of model building and testing.

Our bedrock organizational principle is that every model is a collection of Processes. This core idea allows you to compare models with a single click. You can extract subsystems from complex models and work on them independently. You can combine models with a single click. A searchable model tree structure is always immediately available to allow you to drill down to the details of every element of your diagram.

We think of all models as hypotheses and ProcessDB is specifically designed to test those hypotheses against experimental data.

As much as possible, ProcessDB separates the biology from the experiments. Some modeling philosophies assert that there is no such thing as a model separate from an experiment, but biologists rarely think this way. ProcessDB supports the testing of models, simultaneously, against as many different experimental protocols and data sets as you like.